To portably run an app, you run an app launcher, which in turn runs its associated app using the runtime library. You create app launchers using the JauntePE app, which places the launchers into the root directory of a saved portable package folder.
If you're familiar with how Windows shortcuts work, then you're familiar with how a JPE app launcher works. There are technical and usage differences, but conceptually they are the same thing.
To be continued.